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@@ -0,0 +1,7 b'' | |||
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1 | .. _extensions_rmagic: | |
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2 | ||
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3 | =========== | |
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4 | Rmagic | |
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5 | =========== | |
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6 | ||
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7 | .. automodule:: IPython.extensions.rmagic |
@@ -1,12 +1,35 b'' | |||
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1 | 1 | # -*- coding: utf-8 -*- |
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2 | 2 | """ |
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3 | R related magics. | |
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3 | ====== | |
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4 | Rmagic | |
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5 | ====== | |
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4 | 6 | |
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5 | Author: | |
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6 | * Jonathan Taylor | |
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7 | Magic command interface for interactive work with R via rpy2 | |
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8 | ||
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9 | Usage | |
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10 | ===== | |
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11 | ||
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12 | ``%R`` | |
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13 | ||
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14 | {R_DOC} | |
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15 | ||
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16 | ``%Rpush`` | |
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17 | ||
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18 | {RPUSH_DOC} | |
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19 | ||
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20 | ``%Rpull`` | |
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21 | ||
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22 | {RPULL_DOC} | |
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7 | 23 | |
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8 | 24 | """ |
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9 | 25 | |
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26 | #----------------------------------------------------------------------------- | |
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27 | # Copyright (C) 2012 The IPython Development Team | |
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28 | # | |
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29 | # Distributed under the terms of the BSD License. The full license is in | |
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30 | # the file COPYING, distributed as part of this software. | |
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31 | #----------------------------------------------------------------------------- | |
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32 | ||
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10 | 33 | import sys |
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11 | 34 | import tempfile |
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12 | 35 | from glob import glob |
@@ -46,11 +69,16 b' class RMagics(Magics):' | |||
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46 | 69 | self.cache_display_data = cache_display_data |
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47 | 70 | |
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48 | 71 | self.r = ro.R() |
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49 |
self. |
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72 | self.Rstdout_cache = [] | |
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50 | 73 | self.Rconverter = Rconverter |
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51 | 74 | self.pyconverter = pyconverter |
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52 | 75 | |
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53 | 76 | def eval(self, line): |
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77 | ''' | |
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78 | Parse and evaluate a line with rpy2. | |
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79 | Returns the output to R's stdout() connection | |
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80 | and the value of eval(parse(line)). | |
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81 | ''' | |
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54 | 82 | old_writeconsole = ri.get_writeconsole() |
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55 | 83 | ri.set_writeconsole(self.write_console) |
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56 | 84 | try: |
@@ -64,13 +92,16 b' class RMagics(Magics):' | |||
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64 | 92 | |
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65 | 93 | def write_console(self, output): |
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66 | 94 | ''' |
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67 | A hook to capture R's stdout. | |
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95 | A hook to capture R's stdout in a cache. | |
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68 | 96 | ''' |
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69 |
self. |
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97 | self.Rstdout_cache.append(output) | |
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70 | 98 | |
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71 | 99 | def flush(self): |
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72 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.output]) | |
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73 | self.output = [] | |
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100 | ''' | |
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101 | Flush R's stdout cache to a string, returning the string. | |
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102 | ''' | |
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103 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
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104 | self.Rstdout_cache = [] | |
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74 | 105 | return value |
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75 | 106 | |
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76 | 107 | @skip_doctest |
@@ -80,19 +111,19 b' class RMagics(Magics):' | |||
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80 | 111 | A line-level magic for R that pushes |
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81 | 112 | variables from python to rpy2. The line should be made up |
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82 | 113 | of whitespace separated variable names in the IPython |
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83 |
namespace |
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114 | namespace:: | |
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84 | 115 | |
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85 | In [7]: import numpy as np | |
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116 | In [7]: import numpy as np | |
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86 | 117 | |
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87 | In [8]: X = np.array([4.5,6.3,7.9]) | |
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118 | In [8]: X = np.array([4.5,6.3,7.9]) | |
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88 | 119 | |
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89 | In [9]: X.mean() | |
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90 | Out[9]: 6.2333333333333343 | |
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120 | In [9]: X.mean() | |
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121 | Out[9]: 6.2333333333333343 | |
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91 | 122 | |
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92 | In [10]: %Rpush X | |
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123 | In [10]: %Rpush X | |
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93 | 124 | |
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94 | In [11]: %R mean(X) | |
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95 | Out[11]: array([ 6.23333333]) | |
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125 | In [11]: %R mean(X) | |
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126 | Out[11]: array([ 6.23333333]) | |
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96 | 127 | |
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97 | 128 | ''' |
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98 | 129 | |
@@ -122,6 +153,7 b' class RMagics(Magics):' | |||
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122 | 153 | array(['a', '3', '4'], |
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123 | 154 | dtype='|S1') |
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124 | 155 | |
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156 | ||
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125 | 157 | Notes |
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126 | 158 | ----- |
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127 | 159 | |
@@ -233,12 +265,17 b' class RMagics(Magics):' | |||
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233 | 265 | In [17]: W |
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234 | 266 | Out[17]: array([ 5., 20., 25., 50.]) |
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235 | 267 | |
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236 | If the cell evaluates as False, the resulting value is returned | |
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237 | unless the final line prints something to the console. | |
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238 | If the final line results in a NULL value when evaluated | |
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268 | The return value is determined by these rules: | |
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269 | ||
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270 | * If the cell is not None, the magic returns None. | |
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271 | ||
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272 | * If the cell evaluates as False, the resulting value is returned | |
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273 | unless the final line prints something to the console, in | |
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274 | which case None is returned. | |
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275 | ||
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276 | * If the final line results in a NULL value when evaluated | |
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239 | 277 | by rpy2, then None is returned. |
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240 | 278 | |
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241 | If the cell is not None, the magic returns None. | |
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242 | 279 | |
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243 | 280 | ''' |
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244 | 281 | |
@@ -331,6 +368,13 b' class RMagics(Magics):' | |||
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331 | 368 | if result != ri.NULL: |
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332 | 369 | return self.Rconverter(result) |
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333 | 370 | |
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371 | __doc__ = __doc__.format( | |
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372 | R_DOC = ' '*8 + RMagics.R.__doc__, | |
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373 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, | |
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374 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__ | |
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375 | ) | |
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376 | ||
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377 | ||
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334 | 378 | _loaded = False |
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335 | 379 | def load_ipython_extension(ip): |
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336 | 380 | """Load the extension in IPython.""" |
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